feat: unlock full batch parallel docking

Author: Dinaltium

backend/agents/DockingAgent.py

@@ -66,28 +66,42 @@ async def _execute(self, state: dict) -> dict:
         pose_dir = Path(__file__).parent.parent / "data" / "docked_poses" / session_id
         pose_dir.mkdir(parents=True, exist_ok=True)
 
+        semaphore = asyncio.Semaphore(4)
         results = []
-        for idx, mol in enumerate(molecules[:30], start=1):
-            if state.get("cancelled"): break # Check local flag too
-            
-            smiles = mol.get("smiles")
-            if not smiles: continue
- 
-            energy, pose_meta = await _dock_one_async(
-                smiles, pocket, receptor_pdbqt, exe, mode, log, 
-                pose_dir=pose_dir, pose_id=_pose_id(smiles, idx)
-            )
-            
-            if energy is not None:
-                results.append({
-                    "smiles": smiles,
-                    "compound_name": f"Lead-{len(results)+1}",
-                    "binding_energy": energy,
-                    "cnn_score": pose_meta.get("cnn_score") if pose_meta else None,
-                    "cnn_affinity": pose_meta.get("cnn_affinity") if pose_meta else None,
-                    "method": mode,
-                    "pose_id": pose_meta.get("pose_id") if pose_meta else None
-                })
+
+        async def docked_task(idx, mol_data):
+            async with semaphore:
+                smiles = mol_data.get("smiles")
+                if not smiles: return None
+                
+                energy, pose_meta = await _dock_one_async(
+                    smiles, pocket, receptor_pdbqt, exe, mode, log, 
+                    pose_dir=pose_dir, pose_id=_pose_id(smiles, idx)
+                )
+                
+                # Update progress for EACH completion
+                current_prog = 30 + int((len(results) / len(molecules)) * 60)
+                if hasattr(self, 'update_progress'):
+                    await self.update_progress(current_prog, f"Docking {len(results)+1}/{len(molecules)}...")
+                
+                if energy is not None:
+                    return {
+                        "smiles": smiles,
+                        "compound_name": f"Lead-{idx+1}",
+                        "binding_energy": energy,
+                        "cnn_score": pose_meta.get("cnn_score") if pose_meta else None,
+                        "cnn_affinity": pose_meta.get("cnn_affinity") if pose_meta else None,
+                        "method": mode,
+                        "pose_id": pose_meta.get("pose_id") if pose_meta else None
+                    }
+                return None
+
+        # Execute all tasks
+        tasks = [docked_task(i, m) for i, m in enumerate(molecules)]
+        docking_results_all = await asyncio.gather(*tasks)
+        
+        # Filter out failed ones
+        results = [r for r in docking_results_all if r is not None]
 
         return {"docking_results": sorted(results, key=lambda x: x["binding_energy"])}